Certify, a leading contender to win this year's 1,000 Guineas, will now miss the race after traces of anabolic steroids were found in samples. Photograph: PA

Mahmood al-Zarooni, the trainer at the centre of a horse-doping scandal involving a favourite for one of Britain's most prestigious races, is "co-operating fully" with investigators, the British Horseracing Authority said on Tuesday, after 11 horses trained by him tested positive for anabolic steroids.

The horses, trained by Zarooni at Moulton Paddocks just outside Newmarket, Suffolk, have been banned from competition after testing positive for anabolic steroids during an inspection of the stable by BHA investigators on 9 April. They include Certify, an unbeaten three-year-old filly, who would have been a leading contender for the 1,000 Guineas, one of Britain's five Classics, on 5 May but will now be forced to miss the race. Formal charges against Zarooni are due to be made Wednesday.

Leading bookmakers including Ladbrokes, Coral and William Hill have agreed to refund bets placed on Certify prior to her ban from competition.

Zarooni, 37, trains about 150 horses at Moulton Paddocks, all of which are owned by Godolphin, part of the bloodstock operation of Sheikh Mohammed al-Maktoum, the ruler of Dubai. The sheikh, whose passion for racing dates back to visits to Newmarket while studying at Cambridge in the 1960s, has invested hundreds of millions of pounds in Godolphin since its foundation in 1994, and seen its colours carried to success in dozens of significant races.

Zarooni, who joined Godolphin as one of its two principal trainers in March 2010, has sent out the winners of two British Classics. Blue Bunting, a 16-1 chance, took the 1,000 Guineas at Newmarket in May 2011, while Encke, another outsider at 25-1, won the St Leger at Doncaster in September 2012. He also trained Monterosso to win the Dubai World Cup, the most valuable event in the sport with a first prize of $6m (£4m), in March 2012.

Zarooni is all but certain to be banned from racing for several years when he appears before the BHA's disciplinary committee, probably within the next two weeks. The authority is keen to resolve the case quickly to remove uncertainty from betting markets, and Zarooni has admitted the administration of performance-enhancing drugs, saying it was a "catastrophic error" on his part.

While punishment may be swift for Zarooni, however, the sense of astonishment, and even betrayal, that his actions have caused will persist in racing for many months to come. Positive tests for anabolic steroids after a horse has run in a race are all but unknown, although Howard Johnson, a leading National Hunt trainer, was banned from the sport in 2010 after evidence that steroids had been used in his stable emerged in paperwork found in his office.

Steroids are still viewed as a constant and significant threat to racing's integrity, however, because the effects of their use, such as an increase in lean muscle mass, can persist after the substance has left the horse's system. In a sport in which results can be decided by a nose – about 1cm – the unfair advantage that a horse might gain could be worth many thousands of pounds.

"It is, without doubt, a performance-enhancing drug," said James Given, a vet who runs a racing yard in Yorkshire. "It's not just active while the drug is in the body, and certainly many of these drugs will persist in the body for several months, but it's the effect on the muscle development beyond its natural capacity."

In Newmarket, the centre of British Flat racing since King Charles II instituted regular race meetings in the 1660s, the anger at Zarooni's actions runs deep in the tight-knit racing community.

"It's just hideously disappointing," one resident of the town with close ties to a racing stable said on Tuesday. "We've just finished defending the Grand National, and now we've got to defend ourselves against this.

"It's bad for the sport, it's bad for the horses and bad for those who play by the rules. It's cheating, but it's also sickening from the horse welfare perspective. We know what these things do to humans, and it's just not right, full stop."

Zarooni's sole entry in a race in Britain on Tuesday was declared a non-runner a few hours before the race, but he has two horses entered to race at Wolverhampton and six possible runners – including a filly called Controversy – on Friday.